Big changes in Eigen documentation:

- Organize the documentation into "chapters".
  - Each chapter include many documentation pages, reference pages organized as modules, and a quick reference page.
  - The "Chapters" tree is created using the defgroup/ingroup mechanism, even for the documentation pages (i.e., .dox files for which I added an \eigenManualPage macro that we can switch between \page or \defgroup ).
  - Add a "General topics" entry for all pages that do not fit well in the previous "chapters".
  - The highlevel struture is managed by a new eigendoxy_layout.xml file.
- remove the "index" and quite useless pages (namespace list, class hierarchy, member list, file list, etc.)
- add the javascript search-engine.
- add the "treeview" panel.
- remove \tableofcontents (replace them by a custom \eigenAutoToc macro to be able to easily re-enable if needed).
- add javascript to automatically generate a TOC from the h1/h2 tags of the current page, and put the TOC in the left side panel.
- overload various javascript function generated by doxygen to:
  - remove the root of the treeview
  - remove links to section/subsection from the treeview
  - automatically expand the "Chapters" section
  - automatically expand the current section
  - adjust the height of the treeview to take into account the TOC
- always use the default .css file, eigendoxy.css now only includes our modifications
- use Doxyfile to specify our logo
- remove cross references to unsupported modules (temporarily)

doc/eigendoxy_header.html.in

@@ -3,27 +3,27 @@
 <head>
 <meta http-equiv="Content-Type" content="text/xhtml;charset=UTF-8"/>
 <meta http-equiv="X-UA-Compatible" content="IE=9"/>
+<meta name="generator" content="Doxygen $doxygenversion"/>
 <!--BEGIN PROJECT_NAME--><title>$projectname: $title</title><!--END PROJECT_NAME-->
 <!--BEGIN !PROJECT_NAME--><title>$title</title><!--END !PROJECT_NAME-->
-<link href="$relpath$eigendoxy_tabs.css" rel="stylesheet" type="text/css">
-<!--<link href="$relpath$search/search.css" rel="stylesheet" type="text/css"/>-->
-<!--<script type="text/javaScript" src="$relpath$search/search.js"></script>-->
+<link href="$relpath$tabs.css" rel="stylesheet" type="text/css"/>
 <script type="text/javascript" src="$relpath$jquery.js"></script>
 <script type="text/javascript" src="$relpath$dynsections.js"></script>
 $treeview
 $search
 $mathjax
+<link href="$relpath$$stylesheet"   rel="stylesheet" type="text/css" />
 <link href="$relpath$eigendoxy.css" rel="stylesheet" type="text/css">
-<!--<link href="$relpath$defCss" rel="stylesheet" type="text/css" />-->
+<!-- $extrastylesheet -->
+<script type="text/javascript" src="$relpath$eigen_navtree_hacks.js"></script>
+<!-- <script type="text/javascript"> -->
+<!-- </script> -->
+
 </head>
 <body>
-<!--<body onload='searchBox.OnSelectItem(0);'>-->
 <div id="top"><!-- do not remove this div, it is closed by doxygen! -->
 <!-- <a name="top"></a> -->
 
-<a class="logo" href="http://eigen.tuxfamily.org/">
-<img class="logo" src="Eigen_Silly_Professor_64x64.png" width=64 height=64 alt="Eigen's silly professor"/></a>
-
 <!--BEGIN TITLEAREA-->
 <div id="titlearea">
 <table cellspacing="0" cellpadding="0">
@@ -34,7 +34,7 @@ $mathjax
   <!--END PROJECT_LOGO-->
   <!--BEGIN PROJECT_NAME-->
   <td style="padding-left: 0.5em;">
-   <div id="projectname">$projectname
+   <div id="projectname"><a href="http://eigen.tuxfamily.org">$projectname</a>
    <!--BEGIN PROJECT_NUMBER-->&#160;<span id="projectnumber">$projectnumber</span><!--END PROJECT_NUMBER-->
    </div>
    <!--BEGIN PROJECT_BRIEF--><div id="projectbrief">$projectbrief</div><!--END PROJECT_BRIEF-->
@@ -57,4 +57,5 @@ $mathjax
 </table>
 </div>
 <!--END TITLEAREA-->
-<!-- end header part -->
+<!-- end header part -->
+